Added topics: depend on time/rate - Skipped

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1 VIa- 1 Added topics: depend on time/rate - Skipped a) diffusion rate material moves in medium faster motion more friction affect equilibrium separations like electrophoresis HPLC pharmacological cross blood-brain barrier drug absorption b) charge transfer many reactions are redox move charge in enzyme -- special method-- Marcus theory also move charge in cell through Na + or K + channel signaling, neurobiology, muscle activation, etc. c) Photobiology transfer of energy after excitation light absorption and re-emission (fluorescence) structural changes, energetics, signaling Single molecule enzymology It is popular now to try to study single molecules as they undergo some process, enzyme reaction is a good one We discuss average data for many molecules in sample How differ if look at 1 molecule, enzyme turns over can follow rate of individual steps Idea fluorescent enzyme, changes with substrate Trap enzyme so dilute yet not move, add substrate Signal will stay on various times, depending on turnover

2 VIa- 2 Cholesterol oxidase, S=cholesterol, P=oxidized cholest. Active site has flavin adenine dinucleotide (FAD) catalyse oxidation with O 2 E FAD + S k-1 k 1 E FAD S k 2 k -2 E FADH 2 + P O 2 Observe on/off signal for varying amount of time Plot number of times within t t+δt histogram Results the various enzyme molecules fit MM but had different rates, could be due to different conformers from Tinoco

3 VIa- 3 Photobiology: We will return to basics of absorption and fluorescence at end of course in the spectroscopy section idea: light consists of photons E=hν=hc/λ where ν frequency of light, λ wavelength transmitted energy: I t = I 0 (10) -εbc - intensity is flux: cm -2 s -1 b path in cm, c concentration (molar), ε - absorptivity amount absorbed is then: I abs = I 0 (1-(10) -εbc ) note: (10) -εbc =e -2.3εbc if c is low = [A], then I abs ~I 0 (2.3)εb[A] e -x = 1-x+x 2 /2-... excitation rate: r = d[a]/dt = I abs 1000/b from:1/b~cm -1 & 1000cm 3 /L = I 0 (2303)εb[A]/ b integrate rate: [A] = [A 0 ]exp[-i 0 (2303)εt] - 1 st order Jablonski diagram, like a kinetic mechanism, follow energy Engel p , alternate view, kinetic analogy Table 26.1

4 VIa- 4 Quenching provide alternate energy path, like parallel mech. reduce fluorescence view as yield: I f 0 /I f = 1 + (k q /k f )[Q] - Stern-Volmer plot: I f 0 /I f vs [Q] Lifetime: 1/τ f = k f + k q [Q] Diffusion Engel Chap 24, Tinoco, Chapter 6 Analysis of gas collisions will yield the gas law PV = η R T = N/N 0 R T but in form: PV = 1/3 N m u 2 mean velocity since Kinetic Energy ~ 1/2 m υ 2 ~ 1/2 m u 2 PV = 2/3 n (N 0 1/2 m u 2 ) m u 2 =3k B T PV=nRT ½ T measure average Kinetic Energy RT = 2/3 U tr average trans energy [in solution and big molecules also vibration and rotation] [ collisions relate to translations] temperature average kinetic energy Distribution of energies relate to Probability of any one E i, discrete E i Boltzmann: P j = N j /N = g j e -E j/kt /Σ i g i e -E i/kt each weight by e -E i/kt Maxwell-Boltzmann velocity distribution continuous dp(u) = F(u)du = 4π (m/2πkt) 3/2 u 2 e -mu 2/2kT

5 VIa- 5 can be used to describe collisions and other properties of gases Liquids Diffusion better model J x flow of concentration through area Fick 1st J x = -D (dc/dx) - need concentration gradient if dc/dx constant flow Fick 2 nd ( c/ t) = D ( 2 c/ x 2 ) time dependent gradient vary w/x D determine experimentally from Fick s law (cm 2 s -1 ) relates to distributions: D = x 2 /2t x displacement from initial position reverse time to travel distribution (average) D = k B T/ƒ where ƒ frictional coefficient (Einstein) ƒ = 6π η r η viscosity, r radius (assume spherical) could measure size from D shape means measure ƒ greater than calc ƒ 0 ƒ/ƒ 0 increase: non-sherical, or bind solvent

6 VIa- 6 Sedimentation diffuse in medium gravity drive can be molecule or cellular component (big) gravity bouyant force keep up (velocity depend) F = mg m V 2 ρ g ƒυ = m υ/ t : friction slows ρ = density of medium, V 2 = partial specific vol. Centrifuge increase g gravity acceleration effect = a a = ω 2 x ω frequency, x distribution from center terminal velocity becomes: U t = m(1 V 2 ρ) ω 2 x /ƒ sedimentation coefficient: s = U t /ω 2 x = m(1 V 2 ρ)/ƒ combine with diffusion ƒ = kt/d Mass: M = RTs/D(1 V 2 ρ) in molecular weight Electrophoresis charge molecules move in field u = ZeE/f u/e electrophoretic mobility D diffusion constant small molecule ~10-5 cm 2 s -1 large molecule smaller/slower H ion can hop in water Shows up in pre-exponential M + N k d k -d (M N)* P A d = 4π r MN (D M + D N ) N 0 /1000 N 0 Avogadro & (1000 cm 3 L) r MN encounter distance ~ few Å ~ L mol -1 s -1 for r ~ 4 x 10-8 cm, D ~ 1.5 x 10-5 cm 2 s -1 max rate if E a ~ 0 See Tinoco Table 7.5 / pg. 374 typical rates ions can be faster big molecule slower / even with enzyme